Hi<br><br>I want to build my simulation box as tutorial. However I change "vdwradii.dat" file according to the tutorial liquid 2 mix with liquid 1. What should I do?<br><br>Thanks<br><br>Maria<br><div class="gmail_quote">
On Mon, May 2, 2011 at 5:31 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: Continuation=yes From? (mohsen ramezanpour)<br>
2. adding an identified number of water molecules (Maria Hamilton)<br>
3. Re: adding an identified number of water molecules<br>
(Justin A. Lemkul)<br>
4. adding to liquids in the simulation box: one is in the right<br>
side of the box and the other in the left side (Maria Hamilton)<br>
5. Re: adding to liquids in the simulation box: one is in the<br>
right side of the box and the other in the left side<br>
(Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 2 May 2011 16:57:35 +0430<br>
From: mohsen ramezanpour <<a href="mailto:ramezanpour.mohsen@gmail.com">ramezanpour.mohsen@gmail.com</a>><br>
Subject: Re: [gmx-users] Continuation=yes From?<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTink2HpoTh3%2BHHdgtgWYBa4M25P_SA@mail.gmail.com">BANLkTink2HpoTh3+HHdgtgWYBa4M25P_SA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thank you for your detailed axplain<br>
I understood completely<br>
<br>
On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
<br>
><br>
><br>
> mohsen ramezanpour wrote:<br>
><br>
>> Dear Dr.Justin<br>
>><br>
>> Thank you for your reply<br>
>> My is Protein-ligand,It is have the same conditions as tutorial.I did<br>
>> pull ligand in the z direction.<br>
>> Actualy I found your note about gen_vel ,but I didn't any about<br>
>> Continuation!<br>
>><br>
>><br>
> Not that specific keyword, no, but I do address the general principle about<br>
> continuing these simulations via this very discussion about gen_vel.<br>
><br>
><br>
> You are right,But there is another problem:<br>
>> You have not used any -t option in grompp command (doing umbrella<br>
>> step).<br>
>><br>
>><br>
> Correct. See the discussion on gen_vel that I referenced earlier.<br>
><br>
><br>
> Since we have set Continuation=yes;<br>
>> Can grompp realize from which .cpt (npt.cpt ) it must use ?<br>
>><br>
>><br>
> grompp does not make any choice about what it should use. It takes<br>
> whatever input you give it and assembles a run input file. If you're<br>
> following my procedure (which may or may not necessarily be applicable in<br>
> all cases), then there will NOT be a suitable .cpt file for each starting<br>
> configuration. These configurations were generated using SMD, and .cpt<br>
> files are not written and saved at every frame so you have a corresponding<br>
> one later.<br>
><br>
><br>
> And my last question:<br>
>> Do I need to any .cpt file ? (Because I have set Continuation=yes)<br>
>><br>
>><br>
> Checkpointing and continuation are related, but not identical. The<br>
> "continuation" keyword deals with whether or not constraints are solved<br>
> before the first integration step. It otherwise has nothing to do with the<br>
> thermodynamic state of the system, which is contained in the .cpt file.<br>
><br>
> For your system, as I state in the tutorial, you may want to set "gen_vel =<br>
> yes" in each window (since there is no prior equilibration, which may be a<br>
> problem for some systems, but not the tutorial example). This would<br>
> eliminate the need for a .cpt file.<br>
><br>
> -Justin<br>
><br>
> Thanks in advance<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> On Mon, May 2, 2011 at 3:27 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><mailto:<br>
>> <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>> wrote:<br>
>><br>
>><br>
>><br>
>> mohsen ramezanpour wrote:<br>
>><br>
>> Dear Dr.Justin<br>
>><br>
>> Regarding Umbrella Sampling tutorial:<br>
>><br>
>> The CONTINUATION option in md_umbrella.mdp is YES,<br>
>> and you have noticed : From NPT<br>
>><br>
>> I can't understand it's reason correctly!<br>
>><br>
>><br>
>> This is a meaningless comment. It was left there from copying and<br>
>> pasting files before modifying them. The important part is that<br>
>> "continuation = yes" be set to correctly solve the constraints.<br>
>><br>
>><br>
>> we run a NPT and then Pulling, then extracted some<br>
>> configurations from pull.trr file.<br>
>> I think we must continue from pull.cpt not NPT.cpt<br>
>><br>
>> I mean :<br>
>> grompp -f md_umbrella.mdp ............................. -t<br>
>> pull.cpt is more correct than<br>
>><br>
>> grompp -f md_umbrella.mdp .............................. -t<br>
>> NPT.cpt<br>
>><br>
>> am I right?<br>
>><br>
>><br>
>> In the case of the tutorial, no. There is not a corresponding .cpt<br>
>> file for each configuration generated. If you were to somehow apply<br>
>> the same .cpt file for each configuration, almost certainly some of<br>
>> the windows would blow up because the initial velocities would cause<br>
>> nasty collisions. Note that I discuss the continuation issue,<br>
>> proper settings for gen_vel, etc. in the tutorial, step six.<br>
>><br>
>> -Justin<br>
>><br>
>><br>
>> Thanks in advance for your reply<br>
>><br>
>><br>
>> -- ========================================<br>
>><br>
>> Justin A. Lemkul<br>
>> Ph.D. Candidate<br>
>> ICTAS Doctoral Scholar<br>
>> MILES-IGERT Trainee<br>
>> Department of Biochemistry<br>
>> Virginia Tech<br>
>> Blacksburg, VA<br>
>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
>><br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
>> ========================================<br>
>> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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>><br>
>><br>
>><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 2 May 2011 17:19:00 +0430<br>
From: Maria Hamilton <<a href="mailto:hamilton.maria39@gmail.com">hamilton.maria39@gmail.com</a>><br>
Subject: [gmx-users] adding an identified number of water molecules<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <BANLkTinzfai8AZvEK=<a href="mailto:L%2BFXcc7f9-ABZA4A@mail.gmail.com">L+FXcc7f9-ABZA4A@mail.gmail.com</a>><br>
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<br>
Hi all<br>
<br>
If I want to add a simulation box an identified number of water molecules<br>
what should I do?<br>
In manual I see -nmol and -ci in genbox for insert extra molecules but I<br>
don't know for solvent what should I do?<br>
<br>
Thanks alot<br>
<br>
Best Regards<br>
<br>
Maria<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 02 May 2011 08:51:51 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] adding an identified number of water<br>
molecules<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DBEA8E7.5060308@vt.edu">4DBEA8E7.5060308@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Maria Hamilton wrote:<br>
> Hi all<br>
><br>
> If I want to add a simulation box an identified number of water<br>
> molecules what should I do?<br>
> In manual I see -nmol and -ci in genbox for insert extra molecules but I<br>
> don't know for solvent what should I do?<br>
><br>
<br>
Please read about the -maxsol option. I think you will find it most informative.<br>
<br>
-Justin<br>
<br>
> Thanks alot<br>
><br>
> Best Regards<br>
><br>
> Maria<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 2 May 2011 17:28:47 +0430<br>
From: Maria Hamilton <<a href="mailto:hamilton.maria39@gmail.com">hamilton.maria39@gmail.com</a>><br>
Subject: [gmx-users] adding to liquids in the simulation box: one is<br>
in the right side of the box and the other in the left side<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:BANLkTims9r4KwSSQup_r0wsZUVTO52NOXw@mail.gmail.com">BANLkTims9r4KwSSQup_r0wsZUVTO52NOXw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi all<br>
<br>
<br>
To do this at first I fill my box using "genbox" with one of the liquids as<br>
solvent: I used -cs and I did not used -cp.<br>
and then I used "genbox" again to add the other liquid in it: first liquid<br>
as a solute and the second one is as solvent. But these two liquids gives me<br>
a solution. I want to prevent mixing of them. what should I do?<br>
<br>
Thanks alot<br>
<br>
Regards<br>
<br>
Maria<br>
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<br>
Message: 5<br>
Date: Mon, 02 May 2011 09:00:52 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] adding to liquids in the simulation box: one<br>
is in the right side of the box and the other in the left side<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DBEAB04.9080806@vt.edu">4DBEAB04.9080806@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Maria Hamilton wrote:<br>
> Hi all<br>
><br>
><br>
> To do this at first I fill my box using "genbox" with one of the liquids<br>
> as solvent: I used -cs and I did not used -cp.<br>
> and then I used "genbox" again to add the other liquid in it: first<br>
> liquid as a solute and the second one is as solvent. But these two<br>
> liquids gives me a solution. I want to prevent mixing of them. what<br>
> should I do?<br>
><br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials?highlight=tutorials#Heterogeneous_Systems" target="_blank">http://www.gromacs.org/Documentation/Tutorials?highlight=tutorials#Heterogeneous_Systems</a><br>
<br>
-Justin<br>
<br>
> Thanks alot<br>
><br>
> Regards<br>
><br>
> Maria<br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
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